How to visualize the obtained results (predicted synthetic routes) #8

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opened 2025-10-14 17:07:24 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:07:24 -06:00

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Originally created by @MachineGUN001 on 8/5/2023

hi,
thank you to provide such a good method to predict the synthetic routes.

after running the codes provide in git,

from retro_star.api import RSPlanner

planner = RSPlanner(
    gpu=-1,
    use_value_fn=True,
    iterations=100,
    expansion_topk=50
)

result = planner.plan('CCCC[C@@H](C(=O)N1CCC[C@H]1C(=O)O)[C@@H](F)C(=O)OC')

thus we can got a dict, result, with the contents ({'succ': True, 'time': 40.51955580711365, 'iter': 42, 'routes': 'CC(C)c1ccc(-n2nc(O)c3c(=O)c4ccc(Cl)cc4[nH]c3c2=O)cc1>0.9978>
CC(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1|CC(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1>0.5820>C=C(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1|C=C(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1>0.0841>O=C1c2[nH]c3cc(Cl)ccc3c(=O)c2C(=O)N1Nc1ccc(Br)cc1.C=C(C)B1OC(C)(C)C(C)(C)O1|O=C1c2[nH]c3cc(Cl)ccc3c(=O)c2C(=O)N1Nc1ccc(Br)cc1>0.4156>O=C1OC(=O)c2c1[nH]c1cc(Cl)ccc1c2=O.NNc1ccc(Br)cc1|O=C1OC(=O)c2c1[nH]c1cc(Cl)ccc1c2=O>0.1934>O=C(O)c1[nH]c2cc(Cl)ccc2c(=O)c1C(=O)O|O=C(O)c1[nH]c2cc(Cl)ccc2c(=O)c1C(=O)O>0.0010>O=C(O)c1cc(=O)c2ccc(Cl)cc2[nH]1.O=C=O', 'route_cost': 12.44783463616222, 'route_len': 6})

but How to visualize the obtained result? I have very little knowledge of coding, so I'm not quite sure how to use the moltree approach. Can you provide an illustration of how to do the visualization of the predicted routes?

many thanks,

Shengyang

*Originally created by @MachineGUN001 on 8/5/2023* hi, thank you to provide such a good method to predict the synthetic routes. after running the codes provide in git, ``` from retro_star.api import RSPlanner planner = RSPlanner( gpu=-1, use_value_fn=True, iterations=100, expansion_topk=50 ) result = planner.plan('CCCC[C@@H](C(=O)N1CCC[C@H]1C(=O)O)[C@@H](F)C(=O)OC') ``` thus we can got a dict, result, with the contents ({'succ': True, 'time': 40.51955580711365, 'iter': 42, 'routes': 'CC(C)c1ccc(-n2nc(O)c3c(=O)c4ccc(Cl)cc4[nH]c3c2=O)cc1>0.9978> CC(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1|CC(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1>0.5820>C=C(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1|C=C(C)c1ccc(NN2C(=O)c3[nH]c4cc(Cl)ccc4c(=O)c3C2=O)cc1>0.0841>O=C1c2[nH]c3cc(Cl)ccc3c(=O)c2C(=O)N1Nc1ccc(Br)cc1.C=C(C)B1OC(C)(C)C(C)(C)O1|O=C1c2[nH]c3cc(Cl)ccc3c(=O)c2C(=O)N1Nc1ccc(Br)cc1>0.4156>O=C1OC(=O)c2c1[nH]c1cc(Cl)ccc1c2=O.NNc1ccc(Br)cc1|O=C1OC(=O)c2c1[nH]c1cc(Cl)ccc1c2=O>0.1934>O=C(O)c1[nH]c2cc(Cl)ccc2c(=O)c1C(=O)O|O=C(O)c1[nH]c2cc(Cl)ccc2c(=O)c1C(=O)O>0.0010>O=C(O)c1cc(=O)c2ccc(Cl)cc2[nH]1.O=C=O', 'route_cost': 12.44783463616222, 'route_len': 6}) but How to visualize the obtained result? I have very little knowledge of coding, so I'm not quite sure how to use the moltree approach. Can you provide an illustration of how to do the visualization of the predicted routes? many thanks, Shengyang

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Reference: github/retro_star#8

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